bakpack

package module

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Versions in this module

v0

v0.4.0

Oct 9, 2026

Changes in this version

+ var AnnotationJSONSuffixes = []string

v0.3.0

Aug 11, 2026

Changes in this version

+ type SingleFileSource struct

+ File sourceFile

+ func (s SingleFileSource) Get(ctx context.Context, sample string) (FileRecord, error)

+ func (s SingleFileSource) Order(context.Context) ([]string, error)

+ func (s SingleFileSource) Records(ctx context.Context) ([]FileRecord, error)

+ func (s SingleFileSource) WithSampleID(sampleID string) SingleFileSource

v0.2.0

Jul 6, 2026

Changes in this version

+ func BaktaGFF3(annotation []byte, genome Genome) ([]byte, error)

+ func BaktaGFF3WithOptions(annotation []byte, genome Genome, opts BaktaGFF3Options) ([]byte, error)

+ func SupportedBaktaFeatureTypes() []string

type Archive

+ func (a *Archive) ExtractFiles(ctx context.Context, req ExtractRequest, outputDir string) error

+ type BaktaGFF3Options struct

+ AnnotationOnly bool

+ BakpackVersion string

type ExtractOptions

+ GFF3 bool

+ GFF3AnnotationOnly bool

+ OpenOptions OpenArchiveOptions

type ExtractRequest

+ GFF3 bool

+ GFF3AnnotationOnly bool

type ExtractedSample

+ GFF3 []byte

v0.1.0

Jun 24, 2026

Changes in this version

+ const ArchiveMagic

+ const ArchiveVersion

+ func BuildArchive(ctx context.Context, opts BuildOptions) error

+ func CanonicalJSON(value any) ([]byte, error)

+ func CanonicalJSONSHA256(value any) (string, error)

+ func DecodeJSON(data []byte) (any, error)

+ func ExtractArchive(ctx context.Context, opts ExtractOptions) error

+ func FeatureNT(feature map[string]any, genome Genome) (string, bool)

+ func JSONBytesCanonicalSHA256(data []byte) (string, error)

+ func OpenManifestSources(path string) (FileSource, FileSource, error)

+ func PrettyJSON(value any) ([]byte, error)

+ func SHA256Hex(data []byte) string

+ type AGCGenomeSource struct

+ Command string

+ Path string

+ Threads int

+ func (s AGCGenomeSource) Get(ctx context.Context, sample string) (FileRecord, error)

+ func (s AGCGenomeSource) Order(ctx context.Context) ([]string, error)

+ func (s AGCGenomeSource) Records(ctx context.Context) ([]FileRecord, error)

+ type Archive struct

+ func OpenArchive(ctx context.Context, path string, opts ...OpenArchiveOptions) (*Archive, error)

+ func (a *Archive) Close() error

+ func (a *Archive) Extract(ctx context.Context, req ExtractRequest) ([]ExtractedSample, error)

+ func (a *Archive) Index() ArchiveIndex

+ func (a *Archive) SampleIDs() []string

+ type ArchiveIndex struct

+ ChunkSize int

+ Chunks []ChunkIndex

+ Format string

+ PayloadFormat string

+ Samples []SampleIndex

+ Version int

+ func ReadArchiveIndex(path string) (ArchiveIndex, error)

+ func ReadArchiveIndexContext(ctx context.Context, path string, opts ...OpenArchiveOptions) (ArchiveIndex, error)

+ type BuildOptions struct

+ AnnotationSpoolCompression string

+ Annotations FileSource

+ ChunkSize int

+ Genomes FileSource

+ Order []string

+ OutputPath string

+ XZThreads int

+ type ChunkIndex struct

+ CompressedSize int64

+ FeatureFields []string

+ FeatureSchemas []SchemaIndexEntry

+ FieldCodecs []FieldCodec

+ ID int

+ Offset int64

+ TopKeys []string

+ UncompressedSize int64

+ ValueSchemas []SchemaIndexEntry

+ type DirSource struct

+ Dir string

+ Role string

+ func (s DirSource) Get(ctx context.Context, sample string) (FileRecord, error)

+ func (s DirSource) Order(ctx context.Context) ([]string, error)

+ func (s DirSource) Records(ctx context.Context) ([]FileRecord, error)

+ type ExtractOptions struct

+ ArchivePath string

+ Genome bool

+ Genomes FileSource

+ Original bool

+ OutputDir string

+ Reduced bool

+ Samples []string

+ type ExtractRequest struct

+ Genome bool

+ Genomes FileSource

+ OnSample func(ExtractedSample) error

+ Original bool

+ Reduced bool

+ Samples []string

+ type ExtractedSample struct

+ AnnotationName string

+ GenomeFASTA []byte

+ GenomeName string

+ OriginalJSON []byte

+ OriginalJSONCanonicalSHA256 string

+ ReducedJSON []byte

+ ReducedJSONCanonicalSHA256 string

+ SampleID string

+ type FieldCodec struct

+ Field string

+ Kind string

+ Value any

+ Values []string

+ type FileRecord struct

+ Bytes []byte

+ Name string

+ SampleID string

+ type FileSource interface

+ Get func(context.Context, string) (FileRecord, error)

+ Order func(context.Context) ([]string, error)

+ Records func(context.Context) ([]FileRecord, error)

+ func OpenSource(path, kind, role string) (FileSource, error)

+ type Genome struct

+ Contigs []seqio.SeqRecord

+ Filename string

+ SampleID string

+ func ReadGenome(sampleID, filename string, data []byte) (Genome, error)

+ func (g Genome) Contig(name string) ([]byte, bool)

+ func (g Genome) FASTABytes(wrap int) []byte

+ type JSONChecksums struct

+ CanonicalSHA256 string

+ type ListSource struct

+ Path string

+ Role string

+ func (s ListSource) Get(ctx context.Context, sample string) (FileRecord, error)

+ func (s ListSource) Order(ctx context.Context) ([]string, error)

+ func (s ListSource) Records(ctx context.Context) ([]FileRecord, error)

+ type Manifest struct

+ Entries []ManifestEntry

+ Path string

+ func ReadManifest(path string) (Manifest, error)

+ type ManifestEntry struct

+ AnnotationPath string

+ GenomePath string

+ SampleID string

+ type ManifestSource struct

+ Manifest Manifest

+ Role string

+ func (s ManifestSource) Get(ctx context.Context, sample string) (FileRecord, error)

+ func (s ManifestSource) Order(ctx context.Context) ([]string, error)

+ func (s ManifestSource) Records(ctx context.Context) ([]FileRecord, error)

+ type OpenArchiveOptions struct

+ HTTPClient *http.Client

+ type ReduceResult struct

+ Original JSONChecksums

+ Reduced JSONChecksums

+ ReducedJSON []byte

+ func ReduceBaktaJSON(original []byte, genome Genome) (ReduceResult, error)

+ type RestoreResult struct

+ Original JSONChecksums

+ OriginalJSON []byte

+ func RestoreBaktaJSON(reduced []byte, genome Genome) (RestoreResult, error)

+ type SampleIndex struct

+ AnnotationName string

+ ChunkID int

+ GenomeName string

+ OriginalJSONCanonicalSHA256 string

+ ReducedJSONCanonicalSHA256 string

+ SampleID string

+ type SchemaIndexEntry struct

+ Keys []string

+ SchemaID int

+ type TarXZSource struct

+ Path string

+ Role string

+ func (s TarXZSource) Get(ctx context.Context, sample string) (FileRecord, error)

+ func (s TarXZSource) Order(ctx context.Context) ([]string, error)

+ func (s TarXZSource) Records(ctx context.Context) ([]FileRecord, error)

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